I'am struggling on getting an info about how the NS server creates the virtual directory on the PackageShare. What information does it needs to be able to do so and then is codebase part of that process, if yes is it before or after the IIS virtual directory creation ?

This is a tricky one. All I can offer is that I think it must be the Pacakge Server agent that creates the IIS virtual directory - the Notification Server may not have any rights to the Package Server.

You could just look at a combination of IIS and Altiris log files and the package xml files to try and determine a timeline.